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Microorganisms interact with their surroundings and each other. However, these interactions are complex and difficult to understand. This research presents the utilization of simplified environmental microbial systems from the extremes of life to gain insight into the roles of microbes in diverse processes including biogeochemical cycling and viral infection. The complex mixture of organic compounds within aquatic systems, known as dissolved organic matter (DOM), is an integral component of the global carbon cycle. It is a carbon source for microbial activity and impacts biogeochemical and ecological processes. However, little is known about the release and bioconversion of these compounds. This thesis presents a liquid chromatography coupled mass spectrometry (LCMS) based exometabolomics approach to chemically characterize the interaction between DOM and the representative microbial species that transform it. This work illustrates for the first time the ability to measure the relative abundance of molecular constituents of DOM during heterotrophic bacterial processing. Processing was shown to be dynamic over time, even with only single organism interactions. A LCMS based proxy was established to predict the lability of DOM carbon sources, and the labile nature of the source was shown to be a significant factor in DOM processing by single organisms. Further, the temporal interaction of two ecologically relevant beta-Proteobacteria with DOM from the Cotton Glacier, Antarctica highlight the importance of understanding the diversity of single organism DOM interactions to interpret community level bacterial interactions. LCMS-based 'omics techniques can also be utilized to characterize the changes in protein expression associated with viral infection of hyperthermophilic archaea. Viral-host interactions in Sulfolobus archaeal systems are poorly understood, and exhibit a diversity of regulation patterns. LCMS-based shotgun proteomics was utilized to characterize the temporal response of Sulfolobus islandicus to infection by Sulfolobus islandicus rod-shaped virus (SIRV2). The strengths and weaknesses of label-free protein quantitation techniques were assessed, enabling the detection of the regulation of SIRV2 proteins over time and identification of key host responses to infection. Together these studies show the impact of LCMS based 'omics technologies in bringing new insights into environmental microbial interactions.